Article
Chemistry, Multidisciplinary
Will T. Kaufhold, Wolfgang Pfeifer, Carlos E. Castro, Lorenzo Di Michele
Summary: The study utilizes metadynamics to sample the free energy landscapes of DNA nanostructures and demonstrates its ability to predict the mechanical response of DNA nanodevices. These findings are significant for the design and application of DNA nanostructures.
Article
Chemistry, Multidisciplinary
Michael Scheckenbach, Tom Schubert, Carsten Forthmann, Viktorija Glembockyte, Philip Tinnefeld
Summary: Advancements in DNA nanotechnology and DNA origami techniques have enabled the easy design and synthesis of complex and functional nanostructures. Molecular devices are prone to rapid degradation, so self-repair mechanisms are desirable. By utilizing the self-assembly and reconfigurability of DNA origami nanostructures, self-repair of defects can be induced.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Article
Chemistry, Multidisciplinary
Jiajia Zou, Ashley C. Stammers, Andrea Taladriz-Sender, Jamie M. Withers, Iain Christie, Marina Santana Vega, Badri L. Aekbote, William J. Peveler, David A. Rusling, Glenn A. Burley, Alasdair W. Clark
Summary: An orthogonal, noncovalent approach is presented for the assembly of higher-order DNA origami nanostructures. By incorporating perfluorinated tags into DNA origami tiles, their hierarchical assembly is controlled via fluorous-directed recognition. This integrated catch-and-latch approach combining fluorous effect with base-pairing specificity enables increased assembly efficiency and requires fewer DNA sequences, providing a cheap and efficient means for producing discrete superstructures in DNA nanotechnology.
Article
Chemistry, Multidisciplinary
Xinpei Dai, Xiaoliang Chen, Xinxin Jing, Yinan Zhang, Muchen Pan, Mingqiang Li, Qian Li, Pi Liu, Chunhai Fan, Xiaoguo Liu
Summary: Integrating dissimilar materials at the nanoscale is crucial for modern electronics and optoelectronics. Researchers have developed a DNA origami-encoded strategy for integrating silica-metal heterostructures and revealed the underlying mechanisms. By programming the densities and lengths of protruding dsDNA strands on DNA origami, high site-addressability of material deposition was achieved.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Article
Chemistry, Multidisciplinary
Shuoxing Jiang, Nibedita Pal, Fan Hong, Nour Eddine Fahmi, Huiyu Hu, Matthew Vrbanac, Hao Yan, Nils G. Walter, Yan Liu
Summary: Controlling the nucleation step of a self-assembly system is crucial for engineering structural complexity and dynamic behaviors. This study investigates the inherent dynamics of three general nucleation modes in DNA tile-based self-assembly and reveals temperature-dependent kinetics and a nucleation-growth model are key factors. The assembly of tiles can be externally regulated by the hosting frame and an UV-responsive trigger, offering a general strategy for controlling the self-assembly process.
Article
Chemistry, Multidisciplinary
Yuchen Wang, Anjelica Kucinic, Lilly Des Rosiers, Peter E. Beshay, Nicholas Wile, Michael W. Hudoba, Carlos E. Castro
Summary: DNA origami nanotechnology has potential for diverse applications, but its use in education is limited due to high cost and time requirements. We developed an experiment module for classroom implementation, focusing on a deformable hinge joint, that can be evaluated within 120 minutes using cost-effective equipment. Two beam-based models were presented to describe the joint deformation. This module can broaden access to and interest in the mechanical design of DNA origami.
APPLIED SCIENCES-BASEL
(2023)
Article
Chemistry, Multidisciplinary
Marco Lolaico, Sebbe Blokhuizen, Boxuan Shen, Yang Wang, Bjorn Hogberg
Summary: Interest in wireframe DNA origami has been growing, with different designs and software emerging rapidly. In this study, we enhance the design options for A-trail routed wireframe DNA structures by introducing four-helix bundles. We develop software for designing these structures, successfully create and fold a library of structures, and investigate the mechanical rigidity of the reinforced ones. The scaffold routing allows for easy incorporation of reinforced edges and flexible single helix edges, enabling customization of structure stiffness.
Article
Chemistry, Multidisciplinary
Marco Lolaico, Sebbe Blokhuizen, Boxuan Shen, Yang Wang, Bjorn Hogberg
Summary: In recent years, there has been a growing interest in wireframe DNA origami, with various designs, software, and applications emerging rapidly. This study focuses on increasing the design options for A-trail routed wireframe DNA structures by incorporating four-helix bundles (4HB). The researchers developed software for designing these structures, successfully demonstrated the design and folding of a library of structures, and investigated the mechanical rigidity of the reinforced structures. The scaffold routing technique allows for the easy incorporation of reinforced edges and flexible single helix edges, enabling customization of the desired structure's stiffness. The successful folding of hybrid structures and the characterization of different stiffness levels using computational and experimental approaches were demonstrated.
Article
Chemistry, Multidisciplinary
Jingwen Wang, Junjie Yuan, Jiajia Liu, Haixia Zou, Lin Yang, Hong Chen, Xiangmeng Qu
Summary: DNA self-assembly is a promising method for constructing complex nanostructures. However, the current approach requires separate design and professional operation, limiting its development and application. In this study, a novel point-and-shoot strategy based on enzyme-assisted DNA paper-cutting was proposed to construct planar DNA nanostructures using the same DNA origami as a template. By annealing the long scaffold strand and selected staple strands, planar DNA nanostructures were successfully constructed. This strategy overcomes the complexity limitation of planar DNA nanostructures and simplifies the design and operation process. Overall, this strategy shows great potential for manufacturing DNA nanostructures.
Article
Chemistry, Multidisciplinary
Erik Benson, Rafael Carrascosa Marzo, Jonathan Bath, Andrew J. Turberfield
Summary: Linear actuators based on DNA origami are demonstrated in this paper, providing nanoscale precision through bottom-up assembly at the molecular scale. Two assembly strategies and two positioning strategies are used to control the position of the slider on the rail with high yield and precision. These components have potential applications in molecular machinery and nanoscale manufacture, including programmed chemical synthesis.
Article
Chemistry, Multidisciplinary
Leonie Schneider, Kersten S. Rabe, Carmen M. Dominguez, Christof M. Niemeyer
Summary: This study utilizes DNA nanostructures to create multivalent artificial antigens and investigates the spatial requirements and critical factors for mast cell activation. It reveals the importance of antigen-directed assembly of antibody-receptor complexes in triggering degranulation.
Article
Chemistry, Multidisciplinary
Leonie Schneider, Kersten S. Rabe, Carmen M. Dominguez, Christof M. Niemeyer
Summary: The immunological response of mast cells is regulated by the binding of antigens to IgE antibodies bound to the Fc epsilon RI receptor on the cell membrane surface. However, the organization and structural requirements of these antigen-antibody-receptor complexes at the nanometer scale are not fully understood. In this study, DNA nanostructures were used to generate multivalent artificial antigens, allowing for control over valency and nanoscale architecture. The results showed that the assembly of antibody-receptor complexes is critical for mast cell activation, and the affinity and nanoscale distance between the binding partners have less influence on the activation process.
Article
Chemistry, Multidisciplinary
Yuxiang Dong, Jiliang Liu, Xuanzhao Lu, Jialin Duan, Liqi Zhou, Lizhi Dai, Min Ji, Ningning Ma, Yong Wang, Peng Wang, Jun-Jie Zhu, Qianhao Min, Oleg Gang, Ye Tian
Summary: Self-assembly processes are important for fabricating complexly organized nanomaterials, but often limited in creating structures with multiscale order. In this study, a two-stage assembly strategy is introduced to successfully form complexly organized nanoparticle crystals.
Article
Chemistry, Multidisciplinary
Yong Wang, Xuehui Yan, Zhaoyu Zhou, Ningning Ma, Ye Tian
Summary: DNA nanotechnology allows for the assembly of 3D lattices with complex patterns, but altering their symmetries through non-thermal treatments is challenging. This study demonstrates the synthesis of DNA lattices with switchable shapes upon pH change, using octahedral DNA origami frames. The results show the feasibility of obtaining 3D lattices that respond to external stimuli.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Article
Multidisciplinary Sciences
Lizhi Dai, Xiaoxue Hu, Min Ji, Ningning Ma, Hang Xing, Jun- Jie Zhu, Qianhao Min, Ye Tian
Summary: Harnessing the programmable nature of DNA origami, researchers have demonstrated the ability to control structural features in crystalline materials and achieve different equilibrium phases and shapes using a single DNA origami morphology. By modulating the binding coordination with an allosteric factor, the DNA origami crystals undergo phase transitions and yield diverse crystal systems. This approach opens up new possibilities for developing crystalline materials with tunable properties and accessing a rich phase space.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Chemistry, Multidisciplinary
Yang Yang, Zhenyong Wu, Laurie Wang, Kaifeng Zhou, Kai Xia, Qiancheng Xiong, Longfei Liu, Zhao Zhang, Edwin R. Chapman, Yong Xiong, Thomas J. Melia, Erdem Karatekin, Hongzhou Gu, Chenxiang Lin
Summary: A new sorting technique using cholesterol-modified DNA is reported, which can separate liposomes into six to eight homogeneous populations. These uniform and leak-resistant liposomes are ideal for studying how membrane curvature affects membrane protein activities, benefiting research in membrane biology and the development of liposomal drug-delivery systems.
Article
Chemistry, Multidisciplinary
Qi Shen, Taoran Tian, Qiancheng Xiong, Patrick D. Ellis Fisher, Yong Xiong, Thomas J. Melia, C. Patrick Lusk, Chenxiang Lin
Summary: Researchers have developed a biomimetic construct called NanoTrap using DNA nanotechnology to better understand how nucleoporins in the nuclear pore complex establish a selective barrier. The type of FG motif, grafting density, and spatial arrangement were found to be critical determinants of an effective diffusion barrier, with diffusion barriers formed with cohesive FG interactions dominating in mixed-FG-nup scenarios.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2021)
Article
Biochemistry & Molecular Biology
Ane Landajuela, Martha Braun, Christopher D. A. Rodrigues, Alejandro Martinez-Calvo, Thierry Doan, Florian Horenkamp, Anna Andronicos, Vladimir Shteyn, Nathan D. Williams, Chenxiang Lin, Ned S. Wingreen, David Z. Rudner, Erdem Karatekin
Summary: This study characterized the requirements for FisB-mediated membrane fission in bacteria, revealing the importance of protein cluster formation, lipid binding, and homo-oligomerization. FisB was found to accumulate at the engulfment pole and play a critical role in membrane scission during bacterial cell division.
Article
Biochemical Research Methods
Kenny K. H. Chung, Zhao Zhang, Phylicia Kidd, Yongdeng Zhang, Nathan D. Williams, Bennett Rollins, Yang Yang, Chenxiang Lin, David Baddeley, Joerg Bewersdorf
Summary: Two-color fluorogenic DNA-PAINT introduces self-quenching probes, improving imaging speed 26-fold without the need for optical sectioning.
Review
Chemistry, Multidisciplinary
Yuanchen Dong, Yang Yang, Chenxiang Lin, Dongsheng Liu
Summary: This article introduces the recent progress of the frame-guided assembly (FGA) strategy in the preparation of customized amphiphile assemblies. FGA utilizes various nanomaterials with controlled properties as scaffolds to achieve precise control over the assembly morphology of amphiphiles. Different types of FGA assemblies, including inner-frame, outer-frame, and planar-frame, have distinct advantages and applications. FGA has been applied in liposome engineering, membrane protein incorporation, and drug delivery, showcasing its huge potential in fabricating novel and functional complexes.
ACCOUNTS OF CHEMICAL RESEARCH
(2022)
Article
Multidisciplinary Sciences
Zhenhao Fang, Lei Peng, Renata Filler, Kazushi Suzuki, Andrew McNamara, Qianqian Lin, Paul A. Renauer, Luojia Yang, Bridget Menasche, Angie Sanchez, Ping Ren, Qiancheng Xiong, Madison Strine, Paul Clark, Chenxiang Lin, Albert Ko, Nathan D. Grubaugh, Craig B. Wilen, Sidi Chen
Summary: Researchers have developed an Omicron-specific mRNA vaccine candidate and tested its efficacy in animals. The vaccine shows strong antibody response and acts as a booster to improve the effectiveness of the existing vaccine. Interestingly, the heterologous Omicron booster demonstrates higher neutralization potency against the Omicron variant compared to the homologous booster, with comparable effectiveness against the Delta variant.
NATURE COMMUNICATIONS
(2022)
Article
Multidisciplinary Sciences
Longfei Liu, Qiancheng Xiong, Chun Xie, Frederic Pincet, Chenxiang Lin
Summary: The triggered formation of membrane tubes in response to specific DNA signals allows for spatial and temporal control of membrane dynamics in an artificial system. The conformational change of DNA clamps can modulate the timing, efficiency, and width of vesicle tubulation.
Article
Chemistry, Multidisciplinary
Qi Shen, Qiancheng Xiong, Kaifeng Zhou, Qingzhou Feng, Longfei Liu, Taoran Tian, Chunxiang Wu, Yong Xiong, Thomas J. Melia, C. Patrick Lusk, Chenxiang Lin
Summary: The DNA-origami technique is used to construct transmembrane nanopores with programmable size and functionality. By utilizing pneumolysin, a bacterial toxin that forms ring-like channels on cell membranes, hybrid DNA-protein nanopores are formed, enabling the exchange of macromolecules between liposomes and their environment.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Multidisciplinary Sciences
Wangxi Luo, Vladimir Demidov, Qi Shen, Hugo Girao, Manas Chakraborty, Aleksandr Maiorov, Fazly I. Ataullakhanov, Chenxiang Lin, Helder Maiato, Ekaterina L. Grishchuk
Summary: CLASPs are universal stabilizers of microtubule dynamics, and this study reveals that clusters of human CLASP2 form a load-bearing bond with terminal non-GTP tubulins at the stabilized microtubule tip. This activity relies on the TOG2 domain of CLASP2, which releases its high-affinity bond with non-GTP tubulins when they convert into polymerization-competent GTP-tubulins. The recognition of nucleotide-specific tubulin conformation by CLASP2 and its ability to stabilize non-GTP tubulins contribute to the suppression of catastrophe at freely assembling microtubule ends and the promotion of persistent tubulin assembly at load-bearing tethered ends.
Review
Chemistry, Multidisciplinary
Pengfei Zhan, Andreas Peil, Qiao Jiang, Dongfang Wang, Shikufa Mousavi, Qiancheng Xiong, Qi Shen, Yingxu Shang, Baoquan Ding, Chenxiang Lin, Yonggang Ke, Na Liu
Summary: DNA nanotechnology is an interdisciplinary field that combines physics, chemistry, biology, mathematics, engineering, and materials science. The development of DNA origami technique by Paul Rothemund has greatly advanced the field and led to numerous innovative concepts, models, methodologies, and applications. This review highlights the recent progress in DNA origami-engineered nanomaterials over the past five years and explores the potential research directions. It is believed that the legacy of Nadrian Seeman will continue to inspire interdisciplinary innovations and practical applications in the next decade.
Article
Biochemistry & Molecular Biology
Qi Shen, Qingzhou Feng, Chunxiang Wu, Qiancheng Xiong, Taoran Tian, Shuai Yuan, Jiong Shi, Gregory J. Bedwell, Ran Yang, Christopher Aiken, Alan N. Engelman, C. Patrick Lusk, Chenxiang Lin, Yong Xiong
Summary: Using nuclear pore complex mimics, the authors demonstrate that Nup358 provides a dock for HIV-1 capsid on the cytoplasmic side and Nup153 positions the capsid for NPC entry on the nucleoplasmic side. Nup358 and Nup153 create an affinity gradient to regulate capsid penetration, while Nup62 acts as a final gatekeeper against HIV-1 capsid entry.
NATURE STRUCTURAL & MOLECULAR BIOLOGY
(2023)
Article
Multidisciplinary Sciences
Qi Shen, Sushila Kumari, Chaoyi Xu, Sooin Jang, Jiong Shi, Ryan C. Burdick, Lev Levintov, Qiancheng Xiong, Chunxiang Wu, Swapnil C. Devarkar, Taoran Tian, Therese N. Tripler, Yingxia Hu, Shuai Yuan, Joshua Temple, Qingzhou Feng, Patrick Lusk, Christopher Aiken, Alan N. Engelman, Juan R. Perilla, Vinay K. Pathak, Chenxian Lin, Yong Xiong
Summary: Increasing evidence indicates that the intact HIV-1 capsid enters the nucleus in an assembled form, but the interaction between the cone-shaped capsid and nucleoporins (NUPs) in the nuclear pore complex is not well understood. This study reveals that NUP153 binds to HIV-1 capsid by interacting with the assembled capsid protein (CA) lattice. NUP153 contains a bipartite motif with both canonical and noncanonical interaction modules, where the canonical phenylalanine-glycine (FG) motif engages with the CA hexamer and a previously unidentified triple-arginine (RRR) motif targets the CA tri-hexamer interface in the capsid. Both FG and RRR motifs are important for the nuclear import of HIV-1 cores, and the presence of NUP153 stabilizes tubular CA assemblies in vitro. These findings provide mechanistic evidence for the role of NUP153 in facilitating intact capsid entry into the nucleus.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Cell Biology
Le Peng, Paul A. Renauer, Arya Okten, Zhenha Fang, Jonathan J. Park, Xiaoy Zhou, Qianqia Lin, Matthew B. Dong, Renata Filler, Qiancheng Xiong, Paul Clark, Chenxiang Lin, Craig B. Wilen, Sidi Chen
Summary: Lipid nanoparticle (LNP)-mRNA vaccines provide protection against COVID-19, but breakthrough infections caused by multiple variant lineages are common. This study investigates the immune responses of LNP-mRNAs encoding different SARS-CoV-2 variants and finds that all vaccines induce potent antibody and T cell responses, offering protection against various variant viruses.
CELL REPORTS MEDICINE
(2022)
Article
Multidisciplinary Sciences
Swarup Dey, Chunhai Fan, Kurt Gothelf, Jiang Li, Chenxiang Lin, Longfei Liu, Na Liu, Minke A. D. Nijenhuis, Barbara Sacca, Friedrich C. Simmel, Hao Yan, Pengfei Zhan
Summary: DNA origami technology, a bottom-up method for constructing nanostructures, offers high precision and controllability. It finds wide applications in nanofabrication, nanophotonics, nanoelectronics, catalysis, computation, bioimaging, and more. However, challenges such as size limits, stability issues, and scale of production need to be addressed for further advancement in the field.
NATURE REVIEWS METHODS PRIMERS
(2021)
Article
Chemistry, Multidisciplinary
Nathan D. Williams, Ane Landajuela, Ravi Kiran Kasula, Wenjiao Zhou, John T. Powell, Zhiqun Xi, Farren J. Isaacs, Julien Berro, Derek Toomre, Erdem Karatekin, Chenxiang Lin
